Shatt Al-Arab River (in Basrah province South of Iraq) is approximately 192 km long. It plays a key role in providing water for domestic purposes, irrigation, manufacturing, in addition to shipment. Recently the river suffers from increasing pollution, due to wastes from industries, domestic sewage and agricultural activities that find their way into water sources and result in large scale deterioration of water quality. Investigating the river size and significance, becomes necessary to perform a study to understand the water quality of this river that is considered by some experts as one of the most contaminated in Iraq. This work uses the Water Quality Index (WQI) to describe the pollution level of the river and by using Geographic Information System (GIS) to create WQI map. This study also determines the critical pollutants affecting the river water quality throughout its course. WQI has been formulated making use of several water quality parameters such as pH, temperature, Dissolved Oxygen (DO), Biological Oxygen Demand(BOD5), Chemical Oxygen Demand(COD), Nitrate (NO3-2), Phosphate (PO4-3), Total Dissolved Solids (TDS), Total Suspended Solids (TSS), Turbidity (Tur), and Electrical Conductivity (E.C) which were measured at 37 sites along the river. Bad water quality was observed at the sites of the river branches, near the center of Basrah governorate. Furthermore, it was discovered that the main reason for river pollution was due to the high sewage water discharged into the river, especially river branches and illegal discharges of industrial effluent and sewage.